# Mouse / Mammalian biology domain profile
# Filename (without .yaml) is the domain key: "mouse-mammalian"
# Sources: MGI Gene Nomenclature Guidelines (Sept 2024), ARRIVE 2.0, RRID:IMSR_JAX

name: "Mouse / Mammalian biology"

journals:
  - Cell
  - Nature
  - Science
  - "JCI - Journal of Clinical Investigation"
  - "Nature Communications"
  - "Cell Reports"

# Species
species:
  first_mention: "Mus musculus"
  subsequent: ["the mouse", "mice", "the animals"]
  avoid: "the house mouse Mus musculus"

# Strains — common inbred lines
stocks:
  format: "C57BL/6J"
  rrid_prefix: "RRID:IMSR_JAX_"
  common_strains: ["C57BL/6J", "BALB/cJ", "FVB/NJ", "CD-1", "129S1/SvImJ", "C3H/HeJ", "DBA/2J"]
  description: "Jackson Laboratory (JAX) strain designations"

# Nomenclature — official MGI rules
nomenclature:
  - rule: "Gene symbols italicized (e.g. _Brca1_, _Trp53_)"
  - rule: "Protein symbols uppercase, NOT italicized (e.g. BRCA1, TRP53)"
  - rule: "Gene symbol: first letter uppercase, rest lowercase (e.g. _Wt1_, _Plaur_)"
  - rule: "Recessive phenotype symbols start lowercase (e.g. _w_)"
  - rule: "Transgenes: NOT italicized, format Tg(promoter-gene)Line# (e.g. Tg(Drd2-EGFP)S118Gsat)"
  - rule: "Knockout/knockin allele: _Gene<tm1Labcode>_ (e.g. _Brca1<tm1.1Mlg>_)"
  - rule: "Chromosome designations: uppercase C, no period (Chr 15, not Chr.15)"
  - rule: "Always specify sex of animals studied (male, female, or both)"
  - rule: "Always report age (weeks/months) and weight where relevant"

# Auto-detect keywords
detect_keywords: [mouse, mice, "mus musculus", C57BL, BALB, FVB, JAX, "Jackson Laboratory", knockout, knockin, MGI]

# Reporting standards — ARRIVE 2.0 is mandatory for vertebrate animal research
reporting:
  rrid_required: true
  rrid_types: [antibody, "mouse strain", "cell line"]
  key_resources_table: true
  arrive2: true
  arrive2_field: "biology/animal/mouse"
  arrive2_reference: "Percie du Sert et al. 2020, PLOS Biology"
  arrive2_essential_10:
    - "Study design (groups compared, experimental unit)"
    - "Sample size (exact n per group, total animals, a priori power calc)"
    - "Inclusion and exclusion criteria (a priori, reported exclusions)"
    - "Randomisation (method to generate sequence, confounders minimised)"
    - "Blinding (who was aware of group allocation at each stage)"
    - "Outcome measures (primary and secondary, hypothesis-testing primary)"
    - "Statistical methods (test, software, assumption checks, multiple-testing correction)"
    - "Experimental animals (species, strain and substrain, sex, age or developmental stage, weight, provenance, health/immune status, genetic modification)"
    - "Experimental procedures (what/how/when/how often/where/why, acclimatisation)"
    - "Results (summary/descriptive statistics with variability, effect size with CI)"
  ethical_approval: "Required: IACUC or equivalent committee approval, with protocol number"
  acknowledge_jax: "Mice were obtained from the Jackson Laboratory (RRID:IMSR_JAX)."

# Voice rules
voice:
  introduction: "HIGH assertiveness. State the gap; state the question."
  methods: "HIGHEST assertiveness. No hedging. Detail strain, sex, age, source."
  results: "HIGH assertiveness. State findings directly with n, p, effect size, 95% CI."
  discussion: "Moderate hedging. Speculation only in final paragraph."

# Sex canonical
sex:
  - female
  - male